From d5b8c560f1b0ecea50c321dfce4fbd5e6281c2fe Mon Sep 17 00:00:00 2001
From: Lukas Krupcik <lukas.krupcik@vsb.cz>
Date: Fri, 23 Feb 2024 08:43:13 +0100
Subject: [PATCH] 	new file:  
 g/GROMACS/GROMACS-2023.4-ORCA-5.0.1-OpenMPI-4.1.1-double-precision.eb 	new
 file:   g/GROMACS/GROMACS-2023.4-foss-2022a-CUDA-12.0.0-double-precision.eb 
 new file:   g/GROMACS/GROMACS-2023.4-foss-2022a-CUDA-12.0.0.eb 	new
 file:   g/GROMACS/GROMACS-2023.4-foss-2022a-double-precision-test.eb

---
 ...CA-5.0.1-OpenMPI-4.1.1-double-precision.eb | 39 ++++++++++
 ...foss-2022a-CUDA-12.0.0-double-precision.eb | 77 +++++++++++++++++++
 .../GROMACS-2023.4-foss-2022a-CUDA-12.0.0.eb  | 77 +++++++++++++++++++
 ...2023.4-foss-2022a-double-precision-test.eb | 75 ++++++++++++++++++
 4 files changed, 268 insertions(+)
 create mode 100644 g/GROMACS/GROMACS-2023.4-ORCA-5.0.1-OpenMPI-4.1.1-double-precision.eb
 create mode 100644 g/GROMACS/GROMACS-2023.4-foss-2022a-CUDA-12.0.0-double-precision.eb
 create mode 100644 g/GROMACS/GROMACS-2023.4-foss-2022a-CUDA-12.0.0.eb
 create mode 100644 g/GROMACS/GROMACS-2023.4-foss-2022a-double-precision-test.eb

diff --git a/g/GROMACS/GROMACS-2023.4-ORCA-5.0.1-OpenMPI-4.1.1-double-precision.eb b/g/GROMACS/GROMACS-2023.4-ORCA-5.0.1-OpenMPI-4.1.1-double-precision.eb
new file mode 100644
index 00000000..e0737831
--- /dev/null
+++ b/g/GROMACS/GROMACS-2023.4-ORCA-5.0.1-OpenMPI-4.1.1-double-precision.eb
@@ -0,0 +1,39 @@
+# IT4Innovations
+# BS 2024
+
+easyblock = 'CMakeMake'
+name = 'GROMACS'
+version = '2023.4'
+versionsuffix = '-ORCA-5.0.1-double-precision'
+
+homepage = 'http://www.gromacs.org'
+description = """GROMACS is a versatile package to perform molecular dynamics,
+ i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles."""
+
+toolchain = {'name': 'gompi', 'version': '2020c'}
+import os
+if os.environ.get("CLUSTERNAME") in ["KAROLINA"]:
+   toolchainopts = {'openmp': True, 'usempi': True, 'optarch': 'march=core-avx2'}
+else:
+    toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = ['ftp://ftp.gromacs.org/pub/gromacs/', 'https://ftp.gromacs.org/pub/gromacs/']
+
+sources = [SOURCELOWER_TAR_GZ]
+
+checksums = ['4034a8b5ceca56b193afcc5f598824fd']
+
+builddependencies = [
+    ('CMake', '3.18.4'),
+    ('libxml2', '2.9.10'),
+]
+
+dependencies = [
+    ('Boost', '1.74.0'), 
+    ('FFTW', '3.3.8', '', True),
+    ('ORCA', '5.0.1', '-OpenMPI-4.1.1', True),
+]
+
+configopts = '-DGMX_DOUBLE=ON -DGMX_MPI=ON'
+
+moduleclass = 'bio'
diff --git a/g/GROMACS/GROMACS-2023.4-foss-2022a-CUDA-12.0.0-double-precision.eb b/g/GROMACS/GROMACS-2023.4-foss-2022a-CUDA-12.0.0-double-precision.eb
new file mode 100644
index 00000000..e806c074
--- /dev/null
+++ b/g/GROMACS/GROMACS-2023.4-foss-2022a-CUDA-12.0.0-double-precision.eb
@@ -0,0 +1,77 @@
+# IT4Innovations
+# BS 2024
+
+name = 'GROMACS'
+version = '2023.4'
+versionsuffix = '-CUDA-%(cudaver)s-double-precision'
+
+homepage = 'https://www.gromacs.org'
+description = """
+GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
+Newtonian equations of motion for systems with hundreds to millions of
+particles.
+
+This is a GPU enabled build, containing both MPI and threadMPI binaries.
+
+It also contains the gmxapi extension for the single precision MPI build.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = [
+    'https://ftp.gromacs.org/pub/gromacs/',
+    'ftp://ftp.gromacs.org/pub/gromacs/',
+]
+sources = [SOURCELOWER_TAR_GZ]
+#patches = [
+#    'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch',
+#    'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',
+#]
+checksums = [
+    'e5d6c4d9e7ccacfaccb0888619bd21b5ea8911f82b410e68d6db5d40f695f231',
+#    '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199',
+#    '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1',
+]
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('scikit-build', '0.15.0'),
+]
+
+dependencies = [
+    ('CUDA', '12.0.0', '', SYSTEM),
+    ('UCX-CUDA', '1.12.1', '-CUDA-%(cudaver)s'),
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('networkx', '2.8.4'),
+]
+
+double_precision = "ON"
+#configopts = '-DGMX_DOUBLE=on -DGMX_MPI=on'
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('gmxapi', '0.4.2', {
+        'preinstallopts': 'export CMAKE_ARGS="-DGMX_DOUBLE=on ' + '-DGMX_MPI=on '  + 
+                          '-Dgmxapi_ROOT=%(installdir)s ' +
+                          '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
+        'source_tmpl': 'gromacs-2023.4.tar.gz',
+        'start_dir': 'python_packaging/gmxapi',
+        'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'],
+    }),
+]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+}
+
+moduleclass = 'bio'
diff --git a/g/GROMACS/GROMACS-2023.4-foss-2022a-CUDA-12.0.0.eb b/g/GROMACS/GROMACS-2023.4-foss-2022a-CUDA-12.0.0.eb
new file mode 100644
index 00000000..bed44181
--- /dev/null
+++ b/g/GROMACS/GROMACS-2023.4-foss-2022a-CUDA-12.0.0.eb
@@ -0,0 +1,77 @@
+# IT4Innovations
+# BS 2024
+
+name = 'GROMACS'
+version = '2023.4'
+versionsuffix = '-CUDA-%(cudaver)s'
+
+homepage = 'https://www.gromacs.org'
+description = """
+GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
+Newtonian equations of motion for systems with hundreds to millions of
+particles.
+
+This is a GPU enabled build, containing both MPI and threadMPI binaries.
+
+It also contains the gmxapi extension for the single precision MPI build.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = [
+    'https://ftp.gromacs.org/pub/gromacs/',
+    'ftp://ftp.gromacs.org/pub/gromacs/',
+]
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch',
+    'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',
+]
+checksums = [
+    {'gromacs-2023.4.tar.gz': '4034a8b5ceca56b193afcc5f598824fd'},
+    {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch':
+     '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'},
+    {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch':
+     '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'},
+]
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('scikit-build', '0.15.0'),
+]
+
+dependencies = [
+    ('CUDA', '12.0.0', '', SYSTEM),
+    ('UCX-CUDA', '1.12.1', '-CUDA-%(cudaver)s'),
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('networkx', '2.8.4'),
+]
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('gmxapi', '0.4.2', {
+        'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' +
+                          '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
+        'source_tmpl': 'gromacs-2023.4.tar.gz',
+        'start_dir': 'python_packaging/gmxapi',
+        'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'],
+    }),
+]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+}
+
+configopts = '-DGMX_MPI=on'
+
+moduleclass = 'bio'
diff --git a/g/GROMACS/GROMACS-2023.4-foss-2022a-double-precision-test.eb b/g/GROMACS/GROMACS-2023.4-foss-2022a-double-precision-test.eb
new file mode 100644
index 00000000..4e628c80
--- /dev/null
+++ b/g/GROMACS/GROMACS-2023.4-foss-2022a-double-precision-test.eb
@@ -0,0 +1,75 @@
+# IT4Innovations
+# BS 2024
+
+name = 'GROMACS'
+version = '2023.4'
+versionsuffix = '-double-precision'
+
+homepage = 'https://www.gromacs.org'
+description = """
+GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the
+Newtonian equations of motion for systems with hundreds to millions of
+particles.
+
+This is a GPU enabled build, containing both MPI and threadMPI binaries.
+
+It also contains the gmxapi extension for the single precision MPI build.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = [
+    'https://ftp.gromacs.org/pub/gromacs/',
+    'ftp://ftp.gromacs.org/pub/gromacs/',
+]
+sources = ['gromacs-%(version)s.tar.gz']
+patches = [
+    'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch',
+    'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch',
+]
+checksums = [
+    'e5d6c4d9e7ccacfaccb0888619bd21b5ea8911f82b410e68d6db5d40f695f231',
+    '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199',
+    '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1',
+]
+
+builddependencies = [
+    ('CMake', '3.24.3'),
+    ('scikit-build', '0.15.0'),
+]
+
+dependencies = [
+    ('Python', '3.10.4'),
+    ('SciPy-bundle', '2022.05'),
+    ('networkx', '2.8.4'),
+]
+
+double_precision = "ON"
+configopts = '-DGMX_DOUBLE=ON -DGMX_MPI=ON'
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('gmxapi', '0.4.2', {
+        'preinstallopts': 'export CMAKE_ARGS="-DGMX_DOUBLE=on ' + '-DGMX_MPI=on '  + 
+                          '-Dgmxapi_ROOT=%(installdir)s ' +
+                          '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ',
+        'source_tmpl': 'gromacs-2023.4.tar.gz',
+        'start_dir': 'python_packaging/gmxapi',
+        'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'],
+    }),
+]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+}
+
+moduleclass = 'bio'